Publications

2023

  • Ozcan A, Keskin O, Akbulut BS, Ozbek P, Piperidine-based natural products targeting Type IV pili antivirulence: A computational approach, Journal of Molecular Graphics and Modelling, 2023.
  • Picón-Pagès P, Bosch-Morató M, Subirana L, Rubio-Moscardó F, Guivernau B, Fanlo-Ucar H, Zeylan ME, Senyuz S, Herrera-Fernández V, Vicente R, Fernández-Fernández JM, García-Ojalvo J, Gursoy A, Keskin O, Oliva B, Posas F, de Nadal E, Muñoz FJ, A Genome-Wide Functional Screen Identifies Enhancer and Protective Genes for Amyloid Beta-Peptide Toxicity, International Journal of Molecular Sciences, 2023.
  • Celik E, Ozcan G, Vatansever C, Paerhati E, Kuskucu MA, Dogan O, Cekic SG,

2022

  • Abali Z, Ovek D, Senyuz S, Keskin O, Gursoy A, Protein–Protein‐Binding Interfaces, Protein Interactions: The Molecular Basis of Interactomics, 2022.
  • Lim H, Tsai CJ, Keskin O, Nussinov R, Gursoy A, HMI-PRED 2.0: a biologist-oriented web application for prediction of host–microbe protein–protein interaction by interface mimicry, Bioinformatics, 2022.
  • Ozkan E, Celebi O, Keskin O, Gursoy A, Gursoy-Ozdemir Y, Is Persistent Post-COVID Headache Associated With Protein-Protein Interactions Between Antibodies Against Viral Spike Protein and CGRP Receptor?: A Case Report, Frontiers in Pain Research, 2022.
  • Lim H, Cankara F, Tsai CJ, Keskin O, Nussinov R, Gursoy A, Artificial intelligence approaches to human-microbiome protein–protein interactions, Current Opinion in Structural Biology, 2022.
  • Ovek D, Taweel A, Abali Z, Tezsezen E, Koroglu YE, Tsai CJ, Nussinov R, Keskin O, Gursoy A, SARS-CoV-2 interactome 3D: a web interface for 3D visualization and analysis of SARS-CoV-2–human mimicry and interactions, Bioinformatics, 2022.
  • Ovek D, Abali Z, Zeylan ME, Keskin O, Gursoy A, Tuncbag N, Artificial intelligence based methods for hot spot prediction, Current Opinion in Structural Biology, 2022.
  • Asfuroglu P, Sismanlar-Eyuboglu T, Aslan AT, Gursoy TR, Emiralioglu N, Yalcin E, Kiper N, Sen V, Selimoglu-Sen H, Altintas DU, Ozcan D, Kilinc AA, Cokugras H, Kilic-Baskan A, Yazan H, Erenberk U, Dogan G, Unal G, Yilmaz AI, Keskin O, Arik E, Kucukosmanoglu E, Irmak I, Damadoglu E, Ozturk GK, Gulen F, Basaran AE, Bingol A, Cekic S, Sapan N, Kilic G, Harmanci K, Kose M, Ozdemir A, Harmanci K, Kose M, Ozdemir A, Tugcu GD, Eryilmaz-Polat S, Hangul M, Ozcan G, Gayretli-Aydin ZG, Yuksel H, Topal E, Ozdogan S, Caltepe G, Suleyman A, Can D, Korkmaz-Eren P, Bal CM, Kilic M, Cinel G, Cobanoglu N, Perkcan S, Cakir E, Ozcelik U, Dogru D, The success of the Cystic Fibrosis Registry of Turkey for improvement of patient care, Pediatric pulmonology, 2022.  
  • Cankara F, Senyuz S, Keskin O, Gursoy A, DiPPI: Drugs in Protein-Protein Interaction Interfaces, 15th International Symposium on Health Informatics and Bioinformatics HIBIT’22, 2022.
  • Abali Z, Gursoy A, Keskin O, A dataset of protein-protein interfaces for drug repurposing, 15th International Symposium on Health Informatics and Bioinformatics HIBIT’22, 2022.
  • Eren M, Tunçbağ N, Nussinov R, Jang H, Gursoy A, Keskin O, KRas4B Conformational Differences are Highlighted by Computational Analysis with GNM-ANM, 15th International Symposium on Health Informatics and Bioinformatics HIBIT’22, 2022.

2021

  • Can ND, Basturk E, Kizilboga T, Akcay IM, Dingiloglu B, Tatli O, Acar S, Ozfiliz-Kilbas P, Elbeyli E, Muratcioglu S, Jannuzzi AT, Gursoy A, Keskin O, Doganay HL, Karademir-Yilmaz B, Dinler-Doganay G, Interactome analysis of Bag-1 isoforms reveals novel interaction partners in endoplasmic reticulum-associated degradation, Plos one, 2021.
  • Weako J, Jang H, Keskin O, Nussinov R, Gursoy A, The structural basis of Akt PH domain interaction with calmodulin, Biophysical Journal, 2021.
  • Eren M, Tuncbag N, Jang H, Nussinov R, Gursoy A, Keskin O, Normal mode analysis of KRas4B reveals partner specific dynamics, Journal of Physical Chemistry, 2021.
  • Yapici-Eser H, Koroglu YE, Oztop-Cakmak O, Keskin O, Gursoy A, Gursoy-Ozdemir Y, Neuropsychiatric symptoms of COVID-19 explained by SARS-CoV-2 proteins’ mimicry of human protein interactions, Frontiers in Human Neuroscience, 2021.
  • Nussinov R, Jang H, Gursoy A, Keskin O, Gaponenko V, Inhibition of nonfunctional Ras, Cell chemical biology, 2021.
  • Senyuz S, Jang H, Nussinov R, Keskin O, Gursoy A,  Mechanistic Differences of Activation of Rac1ᴾ²⁹S and Rac1ᴬ¹⁵⁹ⱽ, Journal of physical chemistry, 2021.

2020

  • Gill W, Ozkasap O, Gursoy A, Intelligent Edge Computing: State-of-the-art Techniques and Applications, Signal Processing and Communications Applications Conference, IEEE, 2020.
  • Kosoglu K, Omur ME, Jang H, Nussinov R, Keskin O, Gursoy A, The structural basis of the oncogenic mutant K-Ras4B homodimers. bioRxiv, 2020.
  • Weako J, Uba AI, Keskin O, Gursoy A, Yelekci K, Identification of potential inhibitors of human methionine aminopeptidase (type II) for cancer therapy: Structure-based virtual screening, ADMET prediction and molecular dynamics studies, Computational Biology and Chemistry, 2020.
  • Guven-Maiorov E, Hakouz A, Valjevac S, Keskin O, Tsai C, Gursoy A, Nussinov R, HMI-PRED: A Web Server for Structural Prediction of Host-Microbe Interactions Based on Interface Mimicry, Journal of Molecular Biology, 2020.
  • Morova T, McNeill DR, Lallous N, Gönen M, Dalal K, Wilson DM, Gursoy A, Keskin O, Lack N, Androgen receptor-binding sites are highly mutated in prostate cancer. Nat Commun 11, 832 (2020).
  • Pooley JR, Rivers CA, Kilcooley MT, Paul SN, Cavga AD, Kershaw YM, Muratcioglu S, Gursoy A, Keskin O, Lighman SL, Beyond the heterodimer model for mineralocorticoid and glucocorticoid receptor interactions in nuclei and at DNA. PLoS ONE 15(1): e0227520 (2020)
  • Muratcioglu S, Aydin , Odabasi E, Ozdemir E.S, Firat-Karalar E.N, Jang H,  Tsai C, Nussinov R, Kavakli H, Gursoy A, Keskin O, Oncogenic K-Ras4B Dimerization Enhances Downstream Mitogen-activated Protein Kinase Signaling, Journal of Molecular Biology, 432(4) 2020.
  • Halakou F, Gursoy A, Keskin O, Embedding Alternative Conformations of Proteins in Protein–Protein Interaction Networks, In: Canzar S., Ringeling F. (eds) Protein-Protein Interaction Networks. Methods in Molecular Biology, vol 2074. Humana, New York, NY.

2019

  • Yang X, Cheng H, Chen J, Wang R, Saleh A, Si H, Lee S, Guven-Maiorov E, Keskin O, Gursoy A, Nussinov R, Fang J, Waes CV, Chen Z, Head and Neck Cancers Promote an Inflammatory Transcriptome through Coactivation of Classic and Alternative NF-κB Pathways, Cancer Immunology Research, Volume 7, November 2019, Pages 1760-1774
  • Dincer C, Kaya T, Keskin O, Gursoy A, Tuncbag N, 3D spatial organization and network-guided comparison of mutation profiles in Glioblastoma reveals similarities across patients, PLoS computational biology, Volume 15, 2019
  • Ozdemir ES, Nussinov R, Gursoy A,  Keskin O, Developments in integrative modeling with dynamical interfaces, Current Opinion in Structural Biology, Volume 56, June 2019, Pages 11-17
  • Uba AI, Weako J, Keskin O, Gürsoy A, Yelekçi K, Examining the stability of binding modes of the co-crystallized inhibitors of human HDAC8 by molecular dynamics simulation, Journal of Biomolecular Structure and Dynamics, 2019, Pages 1-10.
  • Cavga AD, Tardu M, Korkmaz T, Keskin O, Ozturk N, Gursoy A, Kavakli IH., Cryptochrome deletion in p53 mutant mice enhances apoptotic and anti-tumorigenic responses to UV damage at the transcriptome level, Functional & integrative genomics, Volume 19, 2019, Pages 729–742.
  • Balci AT, Gumeli C, Hakouz A,Yuret A, Keskin O.,DeepInterface: Protein-protein interface validation using 3D Convolutional Neural Networks, bioRxiv, 617506, 2019
  • Ozdemir ES, Nussinov R, Gursoy A, Keskin O., Developments in integrative modeling with dynamical interfaces, Current Opinion in Structural Biology, Vol 56, 2019,Pages 11-17.

2018

  • Ozdemir ES, Gursoy A, Keskin O., Analysis of single amino acid variations in singlet hot spots of protein–protein interfaces,  Bioinformatics 34 (17), i795-i801
  • Ozdemir ES, Jang H, Gursoy A, Keskin O, Li Z, Sacks DB, Nussinov R., Unraveling the molecular mechanism of interactions of the Rho GTPases Cdc42 and Rac1 with the scaffolding protein IQGAP2, J Biol Chem. 2018 Mar 9;293(10):3685-3699.
  • Ozdemir ES, Jang H, Gursoy A, Keskin O, Nussinov R., Arl2-Mediated Allosteric Release of Farnesylated KRas4B from Shuttling Factor PDEδ, J Phys Chem B. 2018 Aug 2;122(30):7503-7513.

2017

  • Halakou F.,  Kilic E.S, Cukuroglu E., Keskin O.,  Gursoy A.,  Enriching Traditional Protein-protein Interaction Networks with Alternative Conformations of Proteins,  Sci Rep. 2017; 7: 7180.
  • Muratcioglu S, Jang H, Gursoy A, Keskin O, Nussinov R.,  PDEδ Binding to Ras Isoforms Provides a Route to Proper Membrane Localization,  J Phys Chem B. 2017 Jun 22;121(24):5917-5927.
  • Ozgur B, Ozdemir ES, Gursoy A, Keskin O.,  Relation between Protein Intrinsic Normal Mode Weights and Pre-Existing Conformer Populations, J Phys Chem B. 2017 Apr 20;121(15):3686-3700.
  • Tuncbag N, Keskin O, Nussinov R, Gursoy A., Prediction of Protein Interactions by Structural Matching: Prediction of PPI Networks and the Effects of Mutations on PPIs that Combines Sequence and Structural Information, Methods Mol Biol. 2017;1558:255-270.
  • Halakou F, Gursoy A, Kilic ES, Keskin O., Topological, functional, and structural analyses of protein-protein interaction networks of breast cancer lung and brain metastases,  2017 EEE Conference Computational Intelligence in Bioinformatics and Computational Biology (CIBCB).
  • Morova T, Gönen M, A Gursoy, Keskin K, Nathan AL., Androgen receptor binding sites are highly mutated in prostate cancer, bioRxiv, 225433, 2017

2016

  • Kuzu G, Keskin O, Nussinov R, Gursoy A., PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps.  Acta Crystallogr D Struct Biol. 2016 Oct 1;72(Pt 10):1137-1148.
  • Guven-Maiorov E, Keskin O, Gursoy A, VanWaes C, Chen Z, Tsai CJ, Nussinov R., TRAF3 signaling: Competitive binding and evolvability of adaptive viral molecular mimicry., Biochim Biophys Acta. 2016 Nov;1860(11 Pt B):2646-55.
  • Tuncbag N, Gursoy A, Keskin O, Nussinov R., The potential impact of recent developments in three-dimensional quantitative interaction proteomics on structural biology., Expert Rev Proteomics. 2016 May;13(5):447-9.
  • Keskin O, Tuncbag N, Gursoy A., Keskin O, Tuncbag N, Gursoy A., Chem Rev. 2016 Apr 27;116(8):4884-909.
  • Jang H, Muratcioglu S, Gursoy A, Keskin O, Nussinov R., Membrane-associated Ras dimers are isoform-specific: K-Ras dimers differ from H-Ras dimers., Biochem J. 2016 Jun 15;473(12):1719-32.
  • Chavan TS, Muratcioglu S, Marszalek R, Jang H, Keskin O, Gursoy A, Nussinov R, Gaponenko V.,  Plasma membrane regulates Ras signaling networks. Cell Logist. 2016 Feb 18;5(4):e1136374.
  • Nussinov R, Muratcioglu S, Tsai CJ, Jang H, Gursoy A, Keskin O., K-Ras4B/calmodulin/PI3Kα: A promising new adenocarcinoma-specific drug target?,  Expert Opin Ther Targets. 2016 Jul;20(7):831-42.
  • Lu S, Jang H, Muratcioglu S, Gursoy A, Keskin O, Nussinov R, Zhang J.,  Ras Conformational Ensembles, Allostery, and Signaling., Chem Rev. 2016 Jun 8;116(11):6607-65.

2015

  • Muratcioglu S, Guven-Maiorov E, Keskin O, Gursoy A., Advances in template-based protein docking by utilizing interfaces towards completing structural interactome. Curr Opin Struct Biol. 2015 Nov 2;35:87-92.
  • Muratcioglu S, Presman DM, Pooley JR, Grntved L, Hager GL, Nussinov R, Keskin O, Gursoy A., Structural Modeling of GR Interactions with the SWI/SNF Chromatin Remodeling Complex and C/EBP,Biophys J. 2015 Sep 15;109(6):1227-39.
  • Guven-Maiorov E, Keskin O, Gursoy A, Nussinov R., A Structural View of Negative Regulation of the Toll-like Receptor-Mediated Inflammatory Pathway, Biophys J. 2015 Sep 15;109(6):1214-26.
  • Nussinov R, Muratcioglu S, Tsai CJ, Jang H, Gursoy A, Keskin O., The Key Role of Calmodulin in KRAS-Driven Adenocarcinomas, Mol Cancer Res. 2015 Sep;13(9):1265-73.
  • Guven-Maiorov E, Keskin O, Gursoy A, VanWaes C, Chen Z, Tsai CJ, Nussinov R., The Architecture of the TIR Domain Signalosome in the Toll-like Receptor-4 Signaling Pathway, Sci Rep. 2015 Aug 21;5:13128
  • Muratcioglu S, Chavan TS, Freed BC, Jang H, Khavrutskii L, Freed RN, Dyba MA, Stefanisko K, Tarasov SG, Gursoy A, Keskin O, Tarasova NI, Gaponenko V, Nussinov R., GTP- Dependent K-Ras Dimerization, Structure. 2015 Jul 7;23(7):1325-35.
  • Cavga AD, Karahan N, Keskin O, Gursoy A., Taming Oncogenic Signaling at Protein Interfaces: Challenges and Opportunities, Curr Top Med Chem. 2015;15(20):2005-18.
  • Nussinov R, Tsai CJ, Muratcioglu S, Jang H, Gursoy A, Keskin O., Principles of K-Ras effector organization and the role of oncogenic K-Ras in cancer initiation through G1 cell cycle deregulation. Expert Rev Proteomics. 2015 Dec;12(6):669-82

2014

  • Baspinar A, Cukuroglu E, Nussinov R, Keskin O, Gursoy A., PRISM: a web server and repository for prediction of protein-protein interactions and modeling their 3D complexes, Nucleic Acids Res. 2014 Jul;42(Web Server issue):W285-9.
  • Acuner Ozbabacan SE, Gursoy A, Nussinov R, Keskin O. The Structural Pathway of Interleukin 1 (IL-1) Initiated Signaling Reveals Mechanisms of Oncogenic Mutations and SNPs in Inflammation and Cancer. PLoS Comput Biol. 2014 Feb 13;10(2).
  • Cukuroglu E, Gursoy A, Nussinov R, Keskin O. Non-redundant unique interface structures as templates for modeling protein interactions. PLoS One. 2014 Jan 27;9(1).
  • Kuzu G, Keskin O, Nussinov R, Gursoy A. Modeling protein assemblies in the proteome. Mol Cell Proteomics. 2014 Mar;13(3):887-96.
  • Guven-Maiorov E, Acuner-Ozbabacan SE, Keskin O, Gursoy A, Nussinov R., Structural pathways of cytokines may illuminate their roles in regulation of cancer development and immunotherapy. Cancers (Basel). 2014 Mar 25;6(2):663-83.
  • Acuner-Ozbabacan ES, Engin BH, Guven-Maiorov E, Kuzu G, Muratcioglu S, Baspinar A, Chen Z, Van Waes C, Gursoy A, Keskin O, Nussinov R., The structural network of Interleukin-10 and its implications in inflammation and cancer. BMC Genomics. 2014;15 Suppl 4:S2. doi: 10.1186/1471-2164-15-S4-S2.
  • Cukuroglu E, Engin HB, Gursoy A, Keskin O., Hot spots in protein-protein interfaces: towards drug discovery. Prog Biophys Mol Biol. 2014 Nov-Dec;116(2-3):165-73
  • Demircioglu D, Keskin O, Gursoy A., Modeling structural protein interaction networks for betweenness analysis. ISCIS2014 LCNS. 2014:367-76

2013

  • Engin HB, Guney E, Keskin O, Oliva B, Gursoy A.,  Integrating structure to protein-protein interaction networks that drive metastasis to brain and lung in breast cancer. PLoS One. 2013 Nov 22;8(11)
  • Maiorov EG, Keskin O, Ng OH, Ozbek U, Gursoy A.,  Identification of interconnected markers for T-cell acute lymphoblastic leukemia. Biomed Res Int. 2013;2013:210253.
  • Engin HB, Gursoy A, Nussinov R, Keskin O. , Network-Based Strategies Can Help Mono- and Poly-pharmacology Drug Discovery: A Systems Biology View. Curr Pharm Des. 2013 May 22.
  • Guven Maiorov E, Keskin O, Gursoy A, Nussinov R. , The structural network of inflammation and cancer: merits and challenges. Semin Cancer Biol. 2013 Aug;23(4):243-51.
  • An O, Gursoy A, Gurgey A, Keskin O. , Structural and functional analysis of perforin mutations in association with clinical data of familial hemophagocytic lymphohistiocytosis type 2 (FHL2) patients. Protein Sci. 2013 Jun;22(6):823-39.
  • Kuzu G, Gursoy A, Nussinov R, Keskin O. , Exploiting conformational ensembles in modeling protein-protein interactions on the proteome scale. J Proteome Res. 2013 Jun 7;12(6):2641-53.
  • Kar G, Keskin O, Fraternali F, Gursoy A. , Emerging role of the ubiquitin-proteasome system as drug targets. Curr Pharm Des. 2013;19(18):3175-89.

2012

  • Engin HB, Keskin O, Nussinov R, Gursoy A., A strategy based on protein-protein interface motifs may help in identifying drug off-targets. J Chem Inf Model. 2012, Aug 27;52(8):2273-86
  • Kar G, Kuzu G, Keskin O, Gursoy A. , Protein-protein interfaces integrated into interaction networks: implications on drug design. Curr Pharm Des. 2012 May 29.
  • Kuzu G, Keskin O, Gursoy A, Nussinov R. Constructing structural networks of signaling pathways on the proteome scale. Curr Opin Struct Biol. 2012 Jun;22(3):367-77.
  • Acuner Ozbabacan SE, Keskin O, Nussinov R, Gursoy A. , Enriching the human apoptosis pathway by predicting the structures of protein-protein complexes. J Struct Biol. 2012 Sep;179(3):338-46
  • Tuncbag N, Keskin O, Nussinov R, Gursoy A. Fast and accurate modeling of protein-protein interactions by combining template-interface-based docking with flexible refinement. Proteins. 2012 Apr;80(4):1239-49.
  • Kuzu G, Keskin O, Gursoy A, Nussinov R. Expanding the conformational selection paradigm in protein-ligand docking. Methods Mol Biol. 2012;819:59-74.
  • Kar G, Keskin O, Nussinov R, Gursoy A. Human proteome-scale structural modeling of E2-E3 interactions exploiting interface motifs. J Proteome Res. 2012; Feb 3;11(2):1196-207.

2011

  • N. Tuncbag, A. Gursoy, R. Nussinov, O. Keskin, Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM, Nature Protocol, 2011 vol. 6 (9) pp. 1341-54.
  • Cukuroglu E, Gursoy A, Keskin O. HotRegion: a database of predicted hot spot clusters. Nucleic Acids Res. 2012 Jan;40(Database issue):D829-33.
  • Sanli D, Keskin O, Gursoy A, Erman B. Structural cooperativity in histone H3 tail modifications. Protein Sci. 2011 Dec;20(12):1982-90. doi: 10.1002/pro.745.
  • O. Ulucan, O. Keskin, B. Erman, A. Gursoy, A Comparative Molecular Dynamics Study of Methylation State Specificity of JMJD2A, PLos ONE, 2011 vol. 6 (9) pp. e24664
  • S.E.A. Ozbabacan, H.B. Engin, A. Gursoy, O. Keskin, Transient protein-protein interactions, Protein Engineering Design & Selection, 2011 vol. 24 (9) pp. 635-48.
  • N. Tuncbag, A. Gursoy, O. Keskin, Prediction of protein-protein interactions: unifying evolution and structure at protein interfaces, Phys Biol, 2011 vol. 8 (3) pp. 035006.
  • M. Ozboyaci, A. Gursoy, B. Erman, O. Keskin, Molecular recognition of H3/H4 histone tails by the tudor domains of JMJD2A: a comparative molecular dynamics simulations study, PLos ONE, 2011 vol. 6 (3) pp. e14765.

2010

  • G. Kar, O. Keskin, A. Gursoy, N. Nussinov, Allostery and population shift in drug discovery, Current Opinion in Pharmacology, Sep, 2010.
  • S.E.A Ozbabacan, A. Gursoy, O. Keskin, R. Nussinov, Conformational ensembles, signal transduction and residue hot spots: Application to drug discovery, Current Opinion in Drug Discovery and Development, 13(5), pp. 527-537, 2010
  • S. Kalyoncu, O. Keskin, A. Gursoy,Interaction prediction and classification of PDZ domains, BMC Bioinformatics, 11(357), 2010.
  • N. Tuncbag, FS. Salman, O. Keskin, A. Gursoy, Analysis and network representation of hotspots in protein interfaces using minimum cut trees, Protein-Structure Function and Bioinformatics, 78(10), pp. 2283-2294, 2010.
  • EB. Unal, A. Gursoy, B. Erman,VitAL: Viterbi algorithm for de novo peptide design, PLOS One, 5(6), e10926, 2010.
  • N. Tuncbag, O.Keskin, A. Gursoy, HotPoint: hotspot prediction server for protein interfaces, Nucl. Acids. Res. (38) Web Server Issue, W402-W406, 2010.
  • E. Cukuroglu, A. Gursoy, O. Keskin, Analysis of Hot Region Organization in Hub Proteins, Annals of Biomedical Engineering, 38(6), pp. 2068-2078, 2010.

2009

  • G. Kar, A. Gursoy, O. Keskin, Human cancer protein-protein interaction network: a structural perspective, PLOS Computational Biology, 5(12) , e1000601, Dec 2009
  • Tuncbag N, Kar G, Gursoy A, Keskin O,  Nussinov R, Towards inferring time dimensionality in protein_protein interaction networks by integrating structures: the p53 example, Molecular BioSystems, 2009
  • Unal B, Gursoy A, Erman B, Conformational energies and entropies of peptides, and the peptide-protein binding problem, Physical Biology 6, 2009
  • Tuncbag N, Gursoy A, Keskin O, Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy, Bioinformatics, Volume: 25 Issue: 12 Pages: 1513-1520 , 2009
  • Tuncbag N, Kar G, Keskin O, Gursoy A, Nussinov R, A survey of available tools and web servers for analysis of protein-protein interactions and interfaces, Briefings in Bioinformatics, Volume: 10 Issue: 3 Pages: 217-232, 2009.

2008

  • Gursoy A, Keskin O, Nussinov R., Topological properties of protein interaction networks from a structural perspective, Biochemical Society Transactions, Volume: 36 Pages: 1398-1403, 2008
  • Tuncbag N, Gursoy A, Guney E, Keskin O, Nussinov R, Architectures and functional coverage of protein-protein interfaces, Journal of Molecular Biology, Volume: 381 Issue: 3 Pages: 785-802, 2008
  • Keskin, O,  Tuncbag, N,  Gursoy, A, Characterization and prediction of protein interfaces to infer protein-protein interaction networks, Current Pharmaceutical Biotechnology, (9)2, 67-76, 2008.
  • Guney, E, Tuncbag, N, Keskin, O, Gursoy, A, HotSprint: database of computational hot spots in protein interfaces, Nucleic Acid Research, (36)  D662-D666, 2008.
  • O. Keskin, A. Gursoy,, B. Ma, R. Nussinov, Principles of protein-protein interactions: What are the preferred ways for proteins to interact?,Chemical Reviews, (108) 4, 1225-1244, 2008.

2007

  • Keskin O, Gursoy A, Ma B, Nussinov R. Towards drugs targeting multiple proteins in a systems biology approach,  Current Topics in Medicinal Chemistry 7 (10): 943-951 2007
  • L. Ormeci, A. Gursoy, G. Tunca, B. Erman, Computational Basis of Knowledge-Based Conformational Probabilities Derived from Local and Long-Range Interactions in Proteins, Proteins: Structure, Function, and Bioinformatics, 66(1):29-40 , 2007.

2006

  • A. Gursoy, O. Keskin, M. Turkay, B. Erman, Relationships between Unfolded Configurations of Proteins and Dynamics of Folding to the Native State, Journal of Polymer Science Part B: Polymer Physics, Vol. 44, 3667-3678, 2006
  • O. Yogurtcu, E. Erzin, and A. Gursoy, Extracting Gene Regulation Information from Microarray Time-Series Data Using Hidden Markov Model, LNCS Vol.:4263 , Pages:144-153 , 2006, Springer-Verlag

2005

  • U. Ogmen, O. Keskin, S. Aytuna, R.Nussinoiv, A.Gursoy, PRISM: Protein interactions by Structural Matching, Nucleic Acids Research, Vol. 33, Web server issue, pp.W331-W336, (2005). PRISM Web Server
  • A.S. Aytuna, A.Gursoy, O.Keskin, Predictions of protein-protein interactions by combining structure and sequence conservation in protein interfaces, Bioinformatics, Vol. 21. No. 12, pp. 2850-2855, 2005.

2004

  • A. Palazoglu, A. Gursoy, Y. Arkun and  B. Erman, Folding Dynamics of Proteins from Denatured to Native State: Principal Component Analysis, Journal of Computational Biology Dec 2004, Vol. 11, No. 6: 1149-1168.
  • O. Keskin, D. Yuret, A. Gursoy, M. Turkay and B. Erman, Relationships between amino acid sequence and backbone torsion angle preferences, Proteins: Structure, Function, and Bioinformatics, Vol 55 No 4 pp. 992-998, 2004.

2003

  • A. Kocatas, A. Gursoy, R. Cetin-Atalay, Application of Data Mining Techniques to Protein-Protein Interactions“, LNCS Vol 2869 pp. 316-323, 2003  (ISCIS 2003)